Synthetic RNA technologies to control cell fate

 

Hirohide Saito, Kyoto University, CiRA

 

It is important to understand dynamics of cellular networks and develop new biotechnologies to solve the mystery of Life. My scientific research career, to date, has focused on the molecular and cellular events governed by RNA and RNA-protein (RNP) interaction networks, aiming to design synthetic RNA and RNP-based molecules and systems to analyze and control living systems. In this seminar, I would like to introduce our original RNA/RNP technologies, that may facilitate comprehensive understanding of RNA/RNP interaction networks in cells, detection and purification of target cells, and future drug discovery.

 

RNA switch is a synthetic mRNA that can detect miRNAs or proteins expressed in target cells. We developed protein- and microRNA (miRNA) -responsive mRNA switches and control translation of desired transgenes, making it possible to detect and control target cells. Importantly, RNA switches can be used as synthetic mRNA-delivery platform, which enables us to treat cells without genomic damage. We have succeeded in detecting and purifying many cell types, including human iPS cells and differentiated cells, which may be useful for future therapeutic applications.

 

FOREST (Folded RNA element profiling with structural motif library) is a massively parallel assay system with a large-scale RNA structure library to identify functional RNP interactions. FOREST could reveal not only sequences but also RNA structures necessary for the interaction to target proteins. As a proof-of-concept, FOREST discovered multiple RNP interaction networks with quantitative scores, including translational regulatory elements that function in living cells. Moreover, FOREST revealed different binding landscapes of RNA G-quadruplex (rG4) structures-binding proteins and discovered rG4 structures in precursor microRNAs. In addition, from transcripts of HIV-1 genome, long-noncoding RNA, and human 5 ‘UTR library, FOREST identified discrete RNA elements that bind to an EIF3-complex and control translation in cells. This technology may discover RNA/RNP structure-function relationships in a massively parallel manner.

 

References:

[1] Miki K et al; Cell Stem Cell, 2015, 16(6):699-711

[2] Wroblewska L et al; Nature Biotechnology, 2015, 33(8):839

[3] Matsuura S et al; Nature Communications, 2018, 9(1):4847

[4] Endo K et al; Science Advances 2019, 5(8):eaax0835

[5] Nakanishi H et al; Nature Communications, 2020, 10;11(1):1297

[6] Komatsu R et al; Submitted